Variant report

Variant	rs9919531
Chromosome Location	chr11:33006582-33006583
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:33004103..33008077-chr11:33008139..33011033,3	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10454479	1.00[JPT][hapmap];0.85[MEX][hapmap]
rs10767973	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10767977	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835991	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10835996	1.00[ASN][1000 genomes]
rs10835997	1.00[ASN][1000 genomes]
rs10835998	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11032017	1.00[JPT][hapmap]
rs11032058	1.00[ASN][1000 genomes]
rs11032060	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11032072	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11032073	1.00[ASN][1000 genomes]
rs11032074	0.94[ASW][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11032076	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11032083	0.86[EUR][1000 genomes]
rs12224002	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174747	1.00[JPT][hapmap]
rs197703	1.00[JPT][hapmap]
rs197706	1.00[JPT][hapmap]
rs2092657	1.00[ASN][1000 genomes]
rs2249555	1.00[ASN][1000 genomes]
rs2419772	1.00[JPT][hapmap]
rs2419773	1.00[JPT][hapmap]
rs2419783	1.00[ASN][1000 genomes]
rs2664693	1.00[JPT][hapmap]
rs2746036	1.00[ASN][1000 genomes]
rs2746037	1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2786800	1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4755476	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4756355	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4756373	1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4756385	1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs589450	1.00[ASN][1000 genomes]
rs602126	1.00[ASN][1000 genomes]
rs6484610	0.94[ASW][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs652963	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7104368	0.94[ASW][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7108574	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7109890	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7118330	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128509	1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73474587	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7395190	1.00[ASW][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7481878	1.00[ASW][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs761284	1.00[JPT][hapmap]
rs761285	1.00[JPT][hapmap]
rs7941237	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7944318	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7950261	1.00[JPT][hapmap]
rs9943506	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758262	chr11:32714643-33049940	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2759815	chr11:32714643-33049940	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	esv2753057	chr11:32796124-33061724	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	esv2753743	chr11:32796124-33084924	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv1040484	chr11:32951066-33093204	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1046198	chr11:32954100-33075142	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv2762904	chr11:32969258-33586535	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
8	nsv1041149	chr11:32981164-33496670	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv1053823	chr11:32981164-33533356	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv897194	chr11:32993887-33471804	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
11	nsv975354	chr11:33001257-33006621	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9919531	QSER1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:32973200-33008600	Weak transcription	HSMMtube	muscle
2	chr11:32979600-33009400	Weak transcription	Stomach Mucosa	stomach
3	chr11:32990400-33008800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:32996000-33008800	Weak transcription	Ovary	ovary
5	chr11:32996000-33009400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr11:32996000-33010000	Weak transcription	Fetal Intestine Small	intestine
7	chr11:32998200-33007000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr11:32998600-33006800	Weak transcription	HepG2	liver
9	chr11:32998600-33007000	Weak transcription	Fetal Brain Female	brain
10	chr11:32998600-33007800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr11:33000400-33007200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr11:33000400-33010400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr11:33000600-33006800	Weak transcription	K562	blood
14	chr11:33000600-33009600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr11:33001800-33009600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr11:33003800-33022200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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